[gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Ok I tried that and it doesn't work:
There's a fundamental difference between chains/no-chains topology, namely
the existence of peptide bond between chains, and the different protonation
state on the termini.
In the chain-based topology there are several termini, and less peptide
bonds.

This causes the no-chains-tpr to have different number of atoms, and
different protonation states.
I tried using tpbconv to make a backbone-tpr, but it still gets me to
segmentation fault.

So thanks, but I don't think it would work.
-SA

On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching <shay.teaching at gmail.com>wrote:

> Thanks, I'll try that, and post again if it works.
>
>
> On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Shay Teaching wrote:
>>
>>> When I try to work the command on a small portion of the backbone it
>>> seems to work just fine. But when I try the entire backbone (which is
>>> composed of several _separate_ chains) I am getting segmentation fault.
>>> Any workaround for that, so I can use the entire backbone?
>>>
>>
>> Are there chain identifiers separating the proteins?  I don't know if that
>> would cause the problem, but it's possible.  In that case, I'd suggest you
>> start with a coordinate file and topology without chain identifiers and
>> generate a new .tpr file (and then take the backbone atoms only with
>> tpbconv).
>>
>> -Justin
>>
>>  Thanks again,
>>> -Shay
>>>
>>>
>>> On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>    Shay Teaching wrote:
>>>
>>>        Hi all,
>>>        (Gromacs 4.0.7): I am trying to make rms matrix between one Wt
>>>        trajectory and one mutant trajectory using the following command:
>>>
>>>        g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
>>>        wt_backbone.ndx
>>>
>>>        The file wt_backbone.ndx contains the backbone of the protein
>>>        (Backbone indices are identical between wt and mutant).
>>>
>>>        The result is that I am getting a well deserved error saying
>>>        that wt.xtc and mutant.xtc has different number of atoms (the
>>>        tpr itself):
>>>        Fatal error:
>>>        Second trajectory (76128 atoms) does not match the first one
>>>        (76129 atoms)
>>>
>>>        So the question becomes: Is there a (convenient) way to produce
>>>        rms-matrix between wt and mutant?
>>>        Or perhaps circumvent this problem in some other way?
>>>
>>>
>>>    Use trjconv to write out new trajectories containing only backbone
>>>    atoms of each protein, then use tpbconv to write a .tpr file with
>>>    only backbone atoms in it (using index groups, if necessary).  Then
>>>    run g_rms again with these new trajectories and .tpr file.
>>>     Everything should match if the indices are chosen correctly.
>>>
>>>    -Justin
>>>
>>>    --     ==============================**__==========
>>>
>>>    Justin A. Lemkul
>>>    Ph.D. Candidate
>>>    ICTAS Doctoral Scholar
>>>    MILES-IGERT Trainee
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
>>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>    <tel:%28540%29%20231-9080>
>>>
>>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
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>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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